Table_1_A Genetic Network Underlying Rhizome Development in Oryza longistaminata.XLSX

The rhizome is an important organ through which many perennial plants are able to propagate vegetatively. Its ecological role has been thoroughly studied on many grass species while the underlying genetic basis is mainly investigated using a rhizomatous wild rice species—Oryza longistaminata. Previous studies have revealed that the rhizome trait in O. longistaminata is jointly controlled by multiple loci, yet how these loci interact with each other remains elusive. Here, an F2 population derived from Oryza sativa (RD23) and O. longistaminata was used to map loci that affect rhizome-related traits. We identified 13 major-effect loci that may jointly control rhizomatousness in O. longistaminata and a total of 51 quantitative trait loci (QTLs) were identified to affect rhizome abundance. Notably, some of these loci were found to have effects on more than one rhizome-related trait. For each trait, a genetic network was constructed according to the genetic expectations of the identified loci. Furthermore, to gain an overview of the genetic regulation on rhizome development, a comprehensive network integrating all these individual networks was assembled. This network consists of three subnetworks that control different aspects of rhizome expression. Judging from the nodes’ role in the network and their corresponding traits, we speculated that qRHZ-3-1, qRHZ-4, qRHI-2, and qRHI-5 are the key loci for rhizome development. Functional verification using rhizome-free recombinant inbred lines (RILs) suggested that qRHI-2 and qRHI-5, two multi-trait controlling loci that appeared to be critical in our network analyses, are likely both needed for rhizome formation. Our results provide more insights into the genetic basis of rhizome development and may facilitate identification of key rhizome-related genes.

根茎（rhizome）是多数多年生植物实现无性繁殖的重要营养器官。目前学界已在多种禾本科物种中对其生态功能开展了深入研究，而其背后的遗传基础则主要通过根茎类野生稻物种——长雄蕊野生稻（Oryza longistaminata）展开探究。既往研究表明，长雄蕊野生稻的根茎性状由多个位点共同调控，但这些位点间的互作机制仍不明晰。本研究以栽培稻（Oryza sativa RD23）与长雄蕊野生稻构建的F2群体为材料，对影响根茎相关性状的位点进行定位。本研究共鉴定到13个可能共同调控长雄蕊野生稻根茎发生的主效位点，以及51个影响根茎丰度的数量性状位点（quantitative trait loci, QTLs）。值得注意的是，部分位点可同时影响多个根茎相关性状。针对每个性状，本研究基于已鉴定位点的遗传效应构建了遗传调控网络。此外，为全面解析根茎发育的遗传调控机制，本研究整合所有单个性状的调控网络，构建了综合调控网络。该综合网络包含三个子网络，分别调控根茎性状表现的不同维度。基于各节点在网络中的功能及其对应性状，本研究推测qRHZ-3-1、qRHZ-4、qRHI-2与qRHI-5为调控根茎发育的关键位点。通过无根茎重组自交系（recombinant inbred lines, RILs）开展功能验证，结果表明：在网络分析中被鉴定为关键的多性状调控位点qRHI-2与qRHI-5，可能共同参与根茎的形成过程。本研究结果为解析根茎发育的遗传基础提供了新的认知，同时也为后续根茎相关关键基因的挖掘与功能鉴定提供了理论参考。